The editing app that will do what you want isn't FCP...it's Adobe Premiere. It'll take nearly any format of QT or MXF or AVI or MP4 and work with them natively on the timeline.
FCP will not. Just because it is a QT file doesn't mean FCP works well with it. And the potential issues are random...loss of sync in the sequence, when you export, random black frames, sections of black video...etc. So yes, if you want to edit all those clips in FCP, you need to convert to media FCP works with: ProRes, HDV, XDCAM, DVCPRO HD. And all the same frame rate.
Now, if you add a clip to the sequence, and notice that it doesn't fill the screen, you double click on it and adjust the scale until it does.
Shane
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